
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   44 (  176),  selected   44 , name T0349TS550_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS550_3-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    E       3      V      11          1.768
LGA    L       4      L      12          1.454
LGA    L       5      L      13          1.288
LGA    R       6      S      14          0.604
LGA    T       7      A      15          0.604
LGA    N       8      V      16          0.336
LGA    D       9      G      17          0.374
LGA    A      10      A      18          0.508
LGA    V      11      L      19          0.877
LGA    L      12      L      20          1.571
LGA    L      13      D      21          0.762
LGA    S      14      G      22          1.204
LGA    A      15      A      23          3.354
LGA    -       -      D      24           -
LGA    V      16      I      25          2.948
LGA    G      17      G      26          4.862
LGA    A      18      H      27           #
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    H      27      L      28          3.239
LGA    L      28      V      29          2.859
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    V      29      R      47          1.658
LGA    P      45      V      48           -
LGA    R      46      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    R      47      D      53           #
LGA    V      48      D      54           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      L      55          3.639
LGA    D      53      A      56          1.695
LGA    D      54      G      57          3.557
LGA    L      55      A      58          2.907
LGA    A      56      R      59          1.034
LGA    G      57      R      60          1.608
LGA    A      58      L      61          1.105
LGA    R      59      L      62          0.874
LGA    R      60      T      63          1.851
LGA    L      61      D      64          2.048
LGA    L      62      A      65          2.370
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    A      68      R      72          5.213
LGA    H      69      -       -           -
LGA    E      70      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   57    5.0     30    2.32    20.00     39.151     1.239

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.917433 * X  +  -0.397874 * Y  +   0.003627 * Z  +   0.793225
  Y_new =  -0.265165 * X  +  -0.618173 * Y  +  -0.739966 * Z  +   7.357737
  Z_new =   0.296655 * X  +   0.677908 * Y  +  -0.672634 * Z  +   1.101312 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.352290   -0.789303  [ DEG:   134.7763    -45.2237 ]
  Theta =  -0.301188   -2.840405  [ DEG:   -17.2568   -162.7432 ]
  Phi   =  -0.281362    2.860231  [ DEG:   -16.1208    163.8792 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0349TS550_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS550_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   57   5.0   30   2.32   20.00  39.151
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS550_3-D1
PFRMAT TS
TARGET T0349
MODEL 3
PARENT 1veh_A
ATOM      1  N   GLU     3      -5.131  -5.776   9.943  1.00  0.00
ATOM      2  CA  GLU     3      -4.983  -4.843  11.058  1.00  0.00
ATOM      3  C   GLU     3      -3.849  -3.870  10.782  1.00  0.00
ATOM      4  O   GLU     3      -3.832  -2.761  11.316  1.00  0.00
ATOM      5  N   LEU     4      -2.919  -4.305   9.942  1.00  0.00
ATOM      6  CA  LEU     4      -1.773  -3.483   9.594  1.00  0.00
ATOM      7  C   LEU     4      -2.220  -2.378   8.629  1.00  0.00
ATOM      8  O   LEU     4      -1.861  -1.215   8.793  1.00  0.00
ATOM      9  N   LEU     5      -2.999  -2.789   7.635  1.00  0.00
ATOM     10  CA  LEU     5      -3.498  -1.853   6.646  1.00  0.00
ATOM     11  C   LEU     5      -4.430  -0.850   7.323  1.00  0.00
ATOM     12  O   LEU     5      -4.202   0.357   7.259  1.00  0.00
ATOM     13  N   ARG     6      -5.460  -1.389   7.969  1.00  0.00
ATOM     14  CA  ARG     6      -6.424  -0.554   8.665  1.00  0.00
ATOM     15  C   ARG     6      -5.693   0.562   9.389  1.00  0.00
ATOM     16  O   ARG     6      -6.199   1.681   9.494  1.00  0.00
ATOM     17  N   THR     7      -4.506   0.234   9.875  1.00  0.00
ATOM     18  CA  THR     7      -3.706   1.205  10.596  1.00  0.00
ATOM     19  C   THR     7      -3.176   2.292   9.656  1.00  0.00
ATOM     20  O   THR     7      -3.456   3.464   9.852  1.00  0.00
ATOM     21  N   ASN     8      -2.416   1.847   8.663  1.00  0.00
ATOM     22  CA  ASN     8      -1.849   2.768   7.697  1.00  0.00
ATOM     23  C   ASN     8      -2.958   3.647   7.126  1.00  0.00
ATOM     24  O   ASN     8      -2.811   4.863   7.052  1.00  0.00
ATOM     25  N   ASP     9      -4.040   3.003   6.729  1.00  0.00
ATOM     26  CA  ASP     9      -5.169   3.711   6.166  1.00  0.00
ATOM     27  C   ASP     9      -5.492   4.927   7.041  1.00  0.00
ATOM     28  O   ASP     9      -5.586   6.043   6.543  1.00  0.00
ATOM     29  N   ALA    10      -5.661   4.658   8.334  1.00  0.00
ATOM     30  CA  ALA    10      -5.967   5.715   9.280  1.00  0.00
ATOM     31  C   ALA    10      -4.965   6.866   9.133  1.00  0.00
ATOM     32  O   ALA    10      -5.341   7.968   8.752  1.00  0.00
ATOM     33  N   VAL    11      -3.718   6.565   9.457  1.00  0.00
ATOM     34  CA  VAL    11      -2.663   7.554   9.371  1.00  0.00
ATOM     35  C   VAL    11      -2.674   8.192   7.985  1.00  0.00
ATOM     36  O   VAL    11      -2.164   9.288   7.793  1.00  0.00
ATOM     37  N   LEU    12      -3.277   7.473   7.049  1.00  0.00
ATOM     38  CA  LEU    12      -3.361   7.948   5.677  1.00  0.00
ATOM     39  C   LEU    12      -4.563   8.886   5.547  1.00  0.00
ATOM     40  O   LEU    12      -4.558   9.801   4.732  1.00  0.00
ATOM     41  N   LEU    13      -5.569   8.614   6.360  1.00  0.00
ATOM     42  CA  LEU    13      -6.783   9.416   6.349  1.00  0.00
ATOM     43  C   LEU    13      -6.635  10.576   7.333  1.00  0.00
ATOM     44  O   LEU    13      -7.131  11.669   7.079  1.00  0.00
ATOM     45  N   SER    14      -5.964  10.290   8.439  1.00  0.00
ATOM     46  CA  SER    14      -5.741  11.297   9.459  1.00  0.00
ATOM     47  C   SER    14      -5.488  12.664   8.818  1.00  0.00
ATOM     48  O   SER    14      -6.426  13.429   8.596  1.00  0.00
ATOM     49  N   ALA    15      -4.292  11.716   7.555  1.00  0.00
ATOM     50  CA  ALA    15      -3.743  12.249   6.261  1.00  0.00
ATOM     51  C   ALA    15      -4.588  11.949   4.985  1.00  0.00
ATOM     52  O   ALA    15      -5.751  11.532   5.094  1.00  0.00
ATOM     53  N   VAL    16      -3.962  12.046   3.515  1.00  0.00
ATOM     54  CA  VAL    16      -4.746  12.122   2.298  1.00  0.00
ATOM     55  C   VAL    16      -5.465  13.464   2.215  1.00  0.00
ATOM     56  O   VAL    16      -5.418  14.124   1.177  1.00  0.00
ATOM     57  N   GLY    17      -6.118  13.849   3.333  1.00  0.00
ATOM     58  CA  GLY    17      -6.846  15.099   3.397  1.00  0.00
ATOM     59  C   GLY    17      -5.884  16.278   3.532  1.00  0.00
ATOM     60  O   GLY    17      -6.310  17.433   3.523  1.00  0.00
ATOM     61  N   ALA    18      -4.608  15.953   3.644  1.00  0.00
ATOM     62  CA  ALA    18      -3.582  16.973   3.776  1.00  0.00
ATOM     63  C   ALA    18      -2.946  17.269   2.413  1.00  0.00
ATOM     64  O   ALA    18      -2.777  18.426   2.048  1.00  0.00
ATOM     65  N   LEU    19      -2.613  16.198   1.705  1.00  0.00
ATOM     66  CA  LEU    19      -2.000  16.324   0.395  1.00  0.00
ATOM     67  C   LEU    19      -2.845  17.273  -0.460  1.00  0.00
ATOM     68  O   LEU    19      -2.335  18.257  -0.989  1.00  0.00
ATOM     69  N   LEU    20      -4.126  16.937  -0.573  1.00  0.00
ATOM     70  CA  LEU    20      -5.047  17.739  -1.356  1.00  0.00
ATOM     71  C   LEU    20      -4.796  19.221  -1.112  1.00  0.00
ATOM     72  O   LEU    20      -4.638  19.996  -2.053  1.00  0.00
ATOM     73  N   ASP    21      -4.766  19.585   0.167  1.00  0.00
ATOM     74  CA  ASP    21      -4.546  20.966   0.552  1.00  0.00
ATOM     75  C   ASP    21      -3.334  21.532  -0.197  1.00  0.00
ATOM     76  O   ASP    21      -3.360  22.686  -0.635  1.00  0.00
ATOM     77  N   GLY    22      -2.312  20.697  -0.329  1.00  0.00
ATOM     78  CA  GLY    22      -1.100  21.101  -1.019  1.00  0.00
ATOM     79  C   GLY    22      -1.339  21.069  -2.531  1.00  0.00
ATOM     80  O   GLY    22      -1.320  22.099  -3.189  1.00  0.00
ATOM     81  N   HIS    27      -3.468   5.030  -1.118  1.00  0.00
ATOM     82  CA  HIS    27      -2.705   3.823  -0.812  1.00  0.00
ATOM     83  C   HIS    27      -3.365   2.591  -1.423  1.00  0.00
ATOM     84  O   HIS    27      -4.379   2.107  -0.911  1.00  0.00
ATOM     85  N   LEU    28      -2.774   2.113  -2.500  1.00  0.00
ATOM     86  CA  LEU    28      -3.291   0.943  -3.192  1.00  0.00
ATOM     87  C   LEU    28      -2.191  -0.099  -3.379  1.00  0.00
ATOM     88  O   LEU    28      -1.460  -0.065  -4.364  1.00  0.00
ATOM     89  N   VAL    29      -2.101  -0.997  -2.404  1.00  0.00
ATOM     90  CA  VAL    29      -1.103  -2.046  -2.450  1.00  0.00
ATOM     91  C   VAL    29      -0.009  -1.792  -1.429  1.00  0.00
ATOM     92  O   VAL    29       0.454  -0.660  -1.275  1.00  0.00
ATOM    153  N   PRO    45      13.137  22.213  -0.367  1.00  0.00
ATOM    154  CA  PRO    45      13.313  22.212   1.077  1.00  0.00
ATOM    155  C   PRO    45      11.992  21.840   1.762  1.00  0.00
ATOM    156  O   PRO    45      11.943  20.915   2.571  1.00  0.00
ATOM    157  N   ARG    46      10.959  22.595   1.417  1.00  0.00
ATOM    158  CA  ARG    46       9.638  22.355   1.986  1.00  0.00
ATOM    159  C   ARG    46       9.206  20.911   1.728  1.00  0.00
ATOM    160  O   ARG    46       8.692  20.246   2.621  1.00  0.00
ATOM    161  N   ARG    47       9.445  20.476   0.499  1.00  0.00
ATOM    162  CA  ARG    47       9.080  19.122   0.112  1.00  0.00
ATOM    163  C   ARG    47       9.882  18.120   0.952  1.00  0.00
ATOM    164  O   ARG    47       9.309  17.265   1.621  1.00  0.00
ATOM    165  N   VAL    48      11.199  18.267   0.886  1.00  0.00
ATOM    166  CA  VAL    48      12.077  17.389   1.633  1.00  0.00
ATOM    167  C   VAL    48      11.844  17.580   3.132  1.00  0.00
ATOM    168  O   VAL    48      12.313  16.792   3.942  1.00  0.00
ATOM    169  N   LEU    49      11.111  18.641   3.447  1.00  0.00
ATOM    170  CA  LEU    49      10.807  18.949   4.832  1.00  0.00
ATOM    171  C   LEU    49       9.477  18.313   5.242  1.00  0.00
ATOM    172  O   LEU    49       9.408  17.630   6.260  1.00  0.00
ATOM    173  N   VAL    50       8.813  18.782   6.271  1.00  0.00
ATOM    174  CA  VAL    50       7.546  18.251   6.764  1.00  0.00
ATOM    175  C   VAL    50       6.454  18.567   5.814  1.00  0.00
ATOM    176  O   VAL    50       5.272  18.715   6.159  1.00  0.00
ATOM    177  N   HIS    51       6.867  18.706   4.578  1.00  0.00
ATOM    178  CA  HIS    51       5.861  18.803   3.651  1.00  0.00
ATOM    179  C   HIS    51       5.983  17.502   2.867  1.00  0.00
ATOM    180  O   HIS    51       4.981  16.952   2.451  1.00  0.00
ATOM    181  N   GLU    52       7.045  16.792   2.605  1.00  0.00
ATOM    182  CA  GLU    52       6.910  15.635   1.751  1.00  0.00
ATOM    183  C   GLU    52       7.648  14.451   2.388  1.00  0.00
ATOM    184  O   GLU    52       7.034  13.453   2.755  1.00  0.00
ATOM    185  N   ASP    53       8.954  14.595   2.490  1.00  0.00
ATOM    186  CA  ASP    53       9.787  13.561   3.068  1.00  0.00
ATOM    187  C   ASP    53       9.400  13.333   4.535  1.00  0.00
ATOM    188  O   ASP    53       9.277  12.199   4.979  1.00  0.00
ATOM    189  N   ASP    54       9.221  14.448   5.241  1.00  0.00
ATOM    190  CA  ASP    54       8.860  14.389   6.642  1.00  0.00
ATOM    191  C   ASP    54       7.698  13.416   6.873  1.00  0.00
ATOM    192  O   ASP    54       7.679  12.675   7.852  1.00  0.00
ATOM    193  N   LEU    55       6.756  13.450   5.938  1.00  0.00
ATOM    194  CA  LEU    55       5.594  12.573   6.019  1.00  0.00
ATOM    195  C   LEU    55       6.043  11.117   5.958  1.00  0.00
ATOM    196  O   LEU    55       5.808  10.350   6.876  1.00  0.00
ATOM    197  N   ALA    56       6.695  10.784   4.857  1.00  0.00
ATOM    198  CA  ALA    56       7.197   9.430   4.655  1.00  0.00
ATOM    199  C   ALA    56       7.744   8.871   5.971  1.00  0.00
ATOM    200  O   ALA    56       7.608   7.689   6.244  1.00  0.00
ATOM    201  N   GLY    57       8.361   9.755   6.741  1.00  0.00
ATOM    202  CA  GLY    57       8.939   9.364   8.007  1.00  0.00
ATOM    203  C   GLY    57       7.811   9.055   8.995  1.00  0.00
ATOM    204  O   GLY    57       7.795   8.002   9.619  1.00  0.00
ATOM    205  N   ALA    58       6.895  10.013   9.110  1.00  0.00
ATOM    206  CA  ALA    58       5.771   9.857  10.019  1.00  0.00
ATOM    207  C   ALA    58       5.169   8.448   9.916  1.00  0.00
ATOM    208  O   ALA    58       4.956   7.785  10.926  1.00  0.00
ATOM    209  N   ARG    59       4.924   8.029   8.681  1.00  0.00
ATOM    210  CA  ARG    59       4.361   6.711   8.433  1.00  0.00
ATOM    211  C   ARG    59       5.227   5.660   9.133  1.00  0.00
ATOM    212  O   ARG    59       4.768   5.009  10.070  1.00  0.00
ATOM    213  N   ARG    60       6.445   5.518   8.642  1.00  0.00
ATOM    214  CA  ARG    60       7.369   4.553   9.203  1.00  0.00
ATOM    215  C   ARG    60       7.434   4.702  10.719  1.00  0.00
ATOM    216  O   ARG    60       7.294   3.714  11.448  1.00  0.00
ATOM    217  N   LEU    61       7.639   5.940  11.158  1.00  0.00
ATOM    218  CA  LEU    61       7.718   6.224  12.584  1.00  0.00
ATOM    219  C   LEU    61       6.587   5.539  13.346  1.00  0.00
ATOM    220  O   LEU    61       6.836   4.779  14.289  1.00  0.00
ATOM    221  N   LEU    62       5.368   5.818  12.915  1.00  0.00
ATOM    222  CA  LEU    62       4.192   5.241  13.542  1.00  0.00
ATOM    223  C   LEU    62       4.067   3.752  13.203  1.00  0.00
ATOM    224  O   LEU    62       3.995   2.915  14.094  1.00  0.00
ATOM    225  N   ALA    68       7.920   4.623   0.179  1.00  0.00
ATOM    226  CA  ALA    68       6.725   5.033  -0.546  1.00  0.00
ATOM    227  C   ALA    68       7.023   5.022  -2.049  1.00  0.00
ATOM    228  O   ALA    68       8.183   5.066  -2.463  1.00  0.00
ATOM    229  N   HIS    69       5.952   4.969  -2.829  1.00  0.00
ATOM    230  CA  HIS    69       6.077   4.949  -4.278  1.00  0.00
ATOM    231  C   HIS    69       4.841   5.570  -4.924  1.00  0.00
ATOM    232  O   HIS    69       3.753   5.550  -4.342  1.00  0.00
ATOM    233  N   GLU    70       5.034   6.106  -6.122  1.00  0.00
ATOM    234  CA  GLU    70       3.947   6.728  -6.856  1.00  0.00
ATOM    235  C   GLU    70       3.395   5.758  -7.903  1.00  0.00
ATOM    236  O   GLU    70       3.831   5.759  -9.047  1.00  0.00
TER
END
